I’ve been going nuts wondering why my iCloud purchases in iTunes 11 won’t show up. I had the checkbox set to make iTunes show my iCloud purchases, and they were being shown, but they suddenly disappeared.
And, so did the option in iTunes preferences called “Show iTunes in the Cloud Purchases.” It’s not there!
I’m going to go kick the neighbors dog now, and pretend that dog is the product management at Apple.
Update: Others have reported that the fix for this is to log out and log back in of iTunes. But that turn-your-head-and-cough style of workaround probably isn’t intended. But, it does work.

Sign out and back into iTunes and it will fix the issue. That doesn’t say it won’t occur again. But this has been what I have been doing any time it occurs.